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Low level CpG island promoter methylation predicts a poor outcome in adult T-cell acute lymphoblastic leukemia.

Touzart A, Boissel N, Belhocine M, Smith C, Graux C, Latiri M, Lhermitte L, Mathieu EL, Huguet F, Lamant L, Ferrier P, Ifrah N, Macintyre E, Dombret H, Asnafi V, Spicuglia S.

Haematologica. 2019 Sep 19. pii: haematol.2019.223677. doi: 10.3324/haematol.2019.223677. [Epub ahead of print]


2HybridTools, a handy software to facilitate clone identification and mutation mapping from yeast two-hybrid screening.

Cauchy P, Kahn-Perlès B, Ferrier P, Imbert J, Lécine P.

PeerJ. 2019 Jul 3;7:e7245. doi: 10.7717/peerj.7245. eCollection 2019.


Detection of long-range electrostatic interactions between charged molecules by means of fluorescence correlation spectroscopy.

Nardecchia I, Lechelon M, Gori M, Donato I, Preto J, Floriani E, Jaeger S, Mailfert S, Marguet D, Ferrier P, Pettini M.

Phys Rev E. 2017 Aug;96(2-1):022403. doi: 10.1103/PhysRevE.96.022403. Epub 2017 Aug 9.


CD8+ T Cells from Human Neonates Are Biased toward an Innate Immune Response.

Galindo-Albarrán AO, López-Portales OH, Gutiérrez-Reyna DY, Rodríguez-Jorge O, Sánchez-Villanueva JA, Ramírez-Pliego O, Bergon A, Loriod B, Holota H, Imbert J, Hernández-Mendoza A, Ferrier P, Carrillo-de Santa Pau E, Valencia A, Spicuglia S, Santana MA.

Cell Rep. 2016 Nov 15;17(8):2151-2160. doi: 10.1016/j.celrep.2016.10.056.


Pasha: a versatile R package for piling chromatin HTS data.

Fenouil R, Descostes N, Spinelli L, Koch F, Maqbool MA, Benoukraf T, Cauchy P, Innocenti C, Ferrier P, Andrau JC.

Bioinformatics. 2016 Aug 15;32(16):2528-30. doi: 10.1093/bioinformatics/btw206. Epub 2016 Apr 22.


Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells.

Soucie EL, Weng Z, Geirsdóttir L, Molawi K, Maurizio J, Fenouil R, Mossadegh-Keller N, Gimenez G, VanHille L, Beniazza M, Favret J, Berruyer C, Perrin P, Hacohen N, Andrau JC, Ferrier P, Dubreuil P, Sidow A, Sieweke MH.

Science. 2016 Feb 12;351(6274):aad5510. doi: 10.1126/science.aad5510. Epub 2016 Jan 21.


Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation.

Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S, Andrau JC.

Nucleic Acids Res. 2016 May 5;44(8):3567-85. doi: 10.1093/nar/gkv1475. Epub 2015 Dec 15.


Long-Range Control of V(D)J Recombination & Allelic Exclusion: Modeling Views.

Outters P, Jaeger S, Zaarour N, Ferrier P.

Adv Immunol. 2015;128:363-413. doi: 10.1016/ Epub 2015 Sep 19. Review.


[Induction of central tolerance by the factor Aire: molecular and epigenetic regulation].

Lopes N, Ferrier P, Irla M.

Med Sci (Paris). 2015 Aug-Sep;31(8-9):742-7. doi: 10.1051/medsci/20153108012. Epub 2015 Sep 4. Review. French.


Reversal of microRNA-150 silencing disadvantages crizotinib-resistant NPM-ALK(+) cell growth.

Hoareau-Aveilla C, Valentin T, Daugrois C, Quelen C, Mitou G, Quentin S, Jia J, Spicuglia S, Ferrier P, Ceccon M, Giuriato S, Gambacorti-Passerini C, Brousset P, Lamant L, Meggetto F.

J Clin Invest. 2015 Sep;125(9):3505-18. doi: 10.1172/JCI78488. Epub 2015 Aug 10.


Thymic Crosstalk Coordinates Medulla Organization and T-Cell Tolerance Induction.

Lopes N, Sergé A, Ferrier P, Irla M.

Front Immunol. 2015 Jul 20;6:365. doi: 10.3389/fimmu.2015.00365. eCollection 2015. Review.


Transcription-dependent generation of a specialized chromatin structure at the TCRβ locus.

Zacarías-Cabeza J, Belhocine M, Vanhille L, Cauchy P, Koch F, Pekowska A, Fenouil R, Bergon A, Gut M, Gut I, Eick D, Imbert J, Ferrier P, Andrau JC, Spicuglia S.

J Immunol. 2015 Apr 1;194(7):3432-43. doi: 10.4049/jimmunol.1400789. Epub 2015 Mar 2.


Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: numerical study.

Nardecchia I, Spinelli L, Preto J, Gori M, Floriani E, Jaeger S, Ferrier P, Pettini M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Aug;90(2):022703. Epub 2014 Aug 6.


Response to Mark Powell's comments.

Ferrier PM, Buzby JC.

Risk Anal. 2013 Mar;33(3):353-5. doi: 10.1111/risa.12021. No abstract available.


Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or 'when stochasticity completes randomness'.

Jaeger S, Fernandez B, Ferrier P.

Immunology. 2013 Jun;139(2):141-50. doi: 10.1111/imm.12057. Review.


CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters.

Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza JZ, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I, Andrau JC.

Genome Res. 2012 Dec;22(12):2399-408. doi: 10.1101/gr.138776.112. Epub 2012 Oct 25.


Differential responses of immune cells to type I interferon contribute to host resistance to viral infection.

Baranek T, Manh TP, Alexandre Y, Maqbool MA, Cabeza JZ, Tomasello E, Crozat K, Bessou G, Zucchini N, Robbins SH, Vivier E, Kalinke U, Ferrier P, Dalod M.

Cell Host Microbe. 2012 Oct 18;12(4):571-84. doi: 10.1016/j.chom.2012.09.002.


[Deciphering functional activity of TLX homeodomain oncogenes in T-ALL: a clue for a differentiating therapy?].

Asnafi V, Ferrier P.

Med Sci (Paris). 2012 Aug-Sep;28(8-9):708-10. doi: 10.1051/medsci/2012288012. Epub 2012 Aug 22. French. No abstract available.


The economic efficiency of sampling size: the case of beef trim.

Ferrier PM, Buzby JC.

Risk Anal. 2013 Mar;33(3):368-84. doi: 10.1111/j.1539-6924.2012.01874.x. Epub 2012 Jul 25.


Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis.

Preto J, Floriani E, Nardecchia I, Ferrier P, Pettini M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Apr;85(4 Pt 1):041904. Epub 2012 Apr 6.


Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation.

Hintermair C, Heidemann M, Koch F, Descostes N, Gut M, Gut I, Fenouil R, Ferrier P, Flatley A, Kremmer E, Chapman RD, Andrau JC, Eick D.

EMBO J. 2012 Jun 13;31(12):2784-97. doi: 10.1038/emboj.2012.123. Epub 2012 May 1.


TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression.

Dadi S, Le Noir S, Payet-Bornet D, Lhermitte L, Zacarias-Cabeza J, Bergeron J, Villarèse P, Vachez E, Dik WA, Millien C, Radford I, Verhoeyen E, Cosset FL, Petit A, Ifrah N, Dombret H, Hermine O, Spicuglia S, Langerak AW, Macintyre EA, Nadel B, Ferrier P, Asnafi V.

Cancer Cell. 2012 Apr 17;21(4):563-76. doi: 10.1016/j.ccr.2012.02.013.


Characterisation of genome-wide PLZF/RARA target genes.

Spicuglia S, Vincent-Fabert C, Benoukraf T, Tibéri G, Saurin AJ, Zacarias-Cabeza J, Grimwade D, Mills K, Calmels B, Bertucci F, Sieweke M, Ferrier P, Duprez E.

PLoS One. 2011;6(9):e24176. doi: 10.1371/journal.pone.0024176. Epub 2011 Sep 20.


H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S.

EMBO J. 2011 Aug 16;30(20):4198-210. doi: 10.1038/emboj.2011.295.


Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36.

de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, Andrade J, Levezinho H, Gut M, Eick D, Gut I, Andrau JC, Ferrier P, Carmo-Fonseca M.

Nat Struct Mol Biol. 2011 Jul 26;18(9):977-83. doi: 10.1038/nsmb.2123.


Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.

Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC.

Nat Struct Mol Biol. 2011 Jul 17;18(8):956-63. doi: 10.1038/nsmb.2085.


Processing ChIP-chip data: from the scanner to the browser.

Cauchy P, Benoukraf T, Ferrier P.

Methods Mol Biol. 2011;719:251-68. doi: 10.1007/978-1-61779-027-0_12.


Epigenetic regulation of antigen receptor gene rearrangement.

Spicuglia S, Zacarias-Cabeza J, Pekowska A, Ferrier P.

F1000 Biol Rep. 2010 Mar 25;2. pii: 23. doi: 10.3410/B2-23.


Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA.

Jia J, Pekowska A, Jaeger S, Benoukraf T, Ferrier P, Spicuglia S.

BMC Res Notes. 2010 Sep 16;3:240. doi: 10.1186/1756-0500-3-240.


A unique H3K4me2 profile marks tissue-specific gene regulation.

Pekowska A, Benoukraf T, Ferrier P, Spicuglia S.

Genome Res. 2010 Nov;20(11):1493-502. doi: 10.1101/gr.109389.110. Epub 2010 Sep 14.


Epigenetic control of Tcrb gene rearrangement.

Spicuglia S, Pekowska A, Zacarias-Cabeza J, Ferrier P.

Semin Immunol. 2010 Dec;22(6):330-6. doi: 10.1016/j.smim.2010.07.002. Epub 2010 Sep 15. Review.


TCR beta allelic exclusion in dynamical models of V(D)J recombination based on allele independence.

Farcot E, Bonnet M, Jaeger S, Spicuglia S, Fernandez B, Ferrier P.

J Immunol. 2010 Aug 1;185(3):1622-32. doi: 10.4049/jimmunol.0904182. Epub 2010 Jun 28.


Duality of enhancer functioning mode revealed in a reduced TCR beta gene enhancer knockin mouse model.

Bonnet M, Huang F, Benoukraf T, Cabaud O, Verthuy C, Boucher A, Jaeger S, Ferrier P, Spicuglia S.

J Immunol. 2009 Dec 15;183(12):7939-48. doi: 10.4049/jimmunol.0902179.


Molecular genetics at the T-cell receptor beta locus: insights into the regulation of V(D)J recombination.

Bonnet M, Ferrier P, Spicuglia S.

Adv Exp Med Biol. 2009;650:116-32. Review.


V(D)J recombination. Preface.

Ferrier P.

Adv Exp Med Biol. 2009;650:v-vi. No abstract available.


Initiation of V(D)J recombination by Dbeta-associated recombination signal sequences: a critical control point in TCRbeta gene assembly.

Franchini DM, Benoukraf T, Jaeger S, Ferrier P, Payet-Bornet D.

PLoS One. 2009;4(2):e4575. doi: 10.1371/journal.pone.0004575. Epub 2009 Feb 24.


CoCAS: a ChIP-on-chip analysis suite.

Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P.

Bioinformatics. 2009 Apr 1;25(7):954-5. doi: 10.1093/bioinformatics/btp075. Epub 2009 Feb 4.


Coronin-1A links cytoskeleton dynamics to TCR alpha beta-induced cell signaling.

Mugnier B, Nal B, Verthuy C, Boyer C, Lam D, Chasson L, Nieoullon V, Chazal G, Guo XJ, He HT, Rueff-Juy D, Alcover A, Ferrier P.

PLoS One. 2008;3(10):e3467. doi: 10.1371/journal.pone.0003467. Epub 2008 Oct 21.


Genome-wide RNA polymerase II: not genes only!

Koch F, Jourquin F, Ferrier P, Andrau JC.

Trends Biochem Sci. 2008 Jun;33(6):265-73. doi: 10.1016/j.tibs.2008.04.006. Epub 2008 May 6. Review.


Essential function for SWI-SNF chromatin-remodeling complexes in the promoter-directed assembly of Tcrb genes.

Osipovich O, Cobb RM, Oestreich KJ, Pierce S, Ferrier P, Oltz EM.

Nat Immunol. 2007 Aug;8(8):809-16. Epub 2007 Jun 24.


[Alpha/beta versus gamma/delta T cell development: a choice linked to the transcription factor Sox13].

Spicuglia S, Bonnet M, Ferrier P.

Med Sci (Paris). 2007 May;23(5):457-8. French. No abstract available.


In vivo reinsertion of excised episomes by the V(D)J recombinase: a potential threat to genomic stability.

Vanura K, Montpellier B, Le T, Spicuglia S, Navarro JM, Cabaud O, Roulland S, Vachez E, Prinz I, Ferrier P, Marculescu R, Jäger U, Nadel B.

PLoS Biol. 2007 Mar;5(3):e43.


Variations in humanized and defined culture conditions supporting derivation of new human embryonic stem cell lines.

Fletcher JM, Ferrier PM, Gardner JO, Harkness L, Dhanjal S, Serhal P, Harper J, Delhanty J, Brownstein DG, Prasad YR, Lebkowski J, Mandalam R, Wilmut I, De Sousa PA.

Cloning Stem Cells. 2006 Winter;8(4):319-34.


Regulation of TCRbeta gene assembly by a promoter/enhancer holocomplex.

Oestreich KJ, Cobb RM, Pierce S, Chen J, Ferrier P, Oltz EM.

Immunity. 2006 Apr;24(4):381-91.


Regulation of V(D)J recombination.

Spicuglia S, Franchini DM, Ferrier P.

Curr Opin Immunol. 2006 Apr;18(2):158-63. Epub 2006 Feb 3. Review.


Development of a zona-free method of nuclear transfer in the mouse.

Ribas R, Oback B, Ritchie W, Chebotareva T, Ferrier P, Clarke C, Taylor J, Gallagher EJ, Maurício AC, Sousa M, Wilmut I.

Cloning Stem Cells. 2005;7(2):126-38.


Normal immune system development in mice lacking the Deltex-1 RING finger domain.

Storck S, Delbos F, Stadler N, Thirion-Delalande C, Bernex F, Verthuy C, Ferrier P, Weill JC, Reynaud CA.

Mol Cell Biol. 2005 Feb;25(4):1437-45.


Restriction endonuclease accessibility as a determinant of altered chromatin structure.

Hempel WM, Ferrier P.

Methods Mol Biol. 2004;287:53-63.


Potassium permanganate as a probe to map DNA-protein interactions in vivo.

Spicuglia S, Kumar S, Chasson L, Payet-Bornet D, Ferrier P.

J Biochem Biophys Methods. 2004 May 31;59(2):189-94.


Coronin-1 expression in T lymphocytes: insights into protein function during T cell development and activation.

Nal B, Carroll P, Mohr E, Verthuy C, Da Silva MI, Gayet O, Guo XJ, He HT, Alcover A, Ferrier P.

Int Immunol. 2004 Feb;16(2):231-40.


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